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RNA:RNA interaction...
RNA:RNA interaction in ternary complexes resolved by chemical probing
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Banijamali, Elnaz (author)
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Baronti, Lorenzo (author)
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Becker, Walter (author)
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Sajkowska-Kozielewicz, Joanna J. (author)
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Huang, Ting (author)
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Palka, Christina (author)
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- Kosek, David (author)
- Karolinska Institutet
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- Sweetapple, Lara (author)
- Karolinska Institutet
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Müller, Juliane (author)
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Stone, Michael D. (author)
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- Andersson, Emma R. (author)
- Karolinska Institutet
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- Petzold, Katja, 1981- (author)
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden; Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa,Petzold
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(creator_code:org_t)
- 2022-12-20
- 2022
- English.
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In: RNA. - : Cold Spring Harbor Laboratory Press (CSHL). - 1355-8382 .- 1469-9001. ; 29:3, s. 317-329
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://urn.kb.se/re...
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http://kipublication...
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Abstract
Subject headings
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- RNA regulation can be performed by a second targeting RNA molecule, such as in the microRNA regulation mechanism. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) probes the structure of RNA molecules and can resolve RNA:protein interactions, but RNA:RNA interactions have not yet been addressed with this technique. Here, we apply SHAPE to investigate RNA-mediated binding processes in RNA:RNA and RNA:RNA-RBP complexes. We use RNA:RNA binding by SHAPE (RABS) to investigate microRNA-34a (miR-34a) binding its mRNA target, the silent information regulator 1 (mSIRT1), both with and without the Argonaute protein, constituting the RNA-induced silencing complex (RISC). We show that the seed of the mRNA target must be bound to the microRNA loaded into RISC to enable further binding of the compensatory region by RISC, while the naked miR-34a is able to bind the compensatory region without seed interaction. The method presented here provides complementary structural evidence for the commonly performed luciferase-assay-based evaluation of microRNA binding-site efficiency and specificity on the mRNA target site and could therefore be used in conjunction with it. The method can be applied to any nucleic acid-mediated RNA- or RBP-binding process, such as splicing, antisense RNA binding, or regulation by RISC, providing important insight into the targeted RNA structure.
Subject headings
- NATURVETENSKAP -- Biologi -- Biofysik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biophysics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Strukturbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Structural Biology (hsv//eng)
Keyword
- RNA biophysics
- MiR targeting/RISC
- RNA secondary structure
- SHAPE
- RNA:RNA binding
Publication and Content Type
- ref (subject category)
- art (subject category)
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RNA
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- By the author/editor
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Banijamali, Elna ...
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Baronti, Lorenzo
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Becker, Walter
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Sajkowska-Koziel ...
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Huang, Ting
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Palka, Christina
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show more...
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Kosek, David
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Sweetapple, Lara
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Müller, Juliane
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Stone, Michael D ...
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Andersson, Emma ...
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Petzold, Katja, ...
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Biophysics
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Structural Biolo ...
- Articles in the publication
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RNA
- By the university
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Uppsala University
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Karolinska Institutet